X-Git-Url: https://git.donarmstrong.com/?p=don.git;a=blobdiff_plain;f=resume.mdwn;h=6497721cc42c5a14122092a440dc5dea48d989c1;hp=26f2117c4a9c5f41064c589a3bbf1424061e0ad9;hb=HEAD;hpb=8724390025715eb7e143547d7fb0e520e1fd4412 diff --git a/resume.mdwn b/resume.mdwn index 26f2117..43e34c0 100644 --- a/resume.mdwn +++ b/resume.mdwn @@ -1,113 +1,185 @@ [[!meta title="Resumé"]] +# Experience +## Team Lead Data Engineering at Ginkgo Bioworks 2022–Present ++ Lead and manged team of data engineers, system administrators, + statisticians, bioinformaticians, and scientists at the PhD level + working within the AgBio unit of Ginkgo Bioworks. ++ Mentored and coached team members in data science, bioinformatics, + data engineering, and statistics. ++ Key leadership role in successful merger of AgBio unit with Ginkgo, + including all relevant R&D business applications and data-adjacent + systems. + +## Team Lead Data Engineering at Bayer Crop Science 2018–2022 ++ Hired, managed, and developed team of 5+ Data Engineers, Systems + Administrators, and Business Analysts working within the Biologics + R&D unit of Bayer Crop Science enabling data capture, data + integration, and operationalization of data analysis pipelines ++ Developed and supervised implementation of data capture, + integration, and analysis strategies to increase the value of + genomics, metabolomics, transcriptomics, spectroscopic, phenotypic + (/in vitro/ and /in planta/), and fermentation/formulation process + data for discovery and development ++ Lead the development of multiple systems while coaching, mentoring, + and developing developers and engineers ++ Served as a key collaborator on multiple cross-function and + cross-divisional projects, including leading the architecture of a + life science collaboration using serverless architecture to provide + machine-learning estimates of critical parameters from + spectrographic measurements ++ Established and developed network of internal and external contacts + for technical implementation of Bayer program goals. + +## Debian Developer 2004–Present ++ Maintained, managed configurations, and resolved issues in multiple + packages written in R, perl, python, scheme, C++, and C. ++ Resolved technical conflicts, developed technical standards, and + provided leadership as the elected chair of the Technical Committee. ++ Developer of [Debbugs](https://bugs.debian.org), a perl and SQL-based issue-tracker with ≥ 100 + million entries with web, REST, and SOAP interfaces. ++ Provided vendor-level support for complex systems integration issues + on Debian GNU/Linux systems. + +## Research Scientist at UIUC 2015–2017 ++ Planning, design, organization, execution, and analysis of multiple + complex epidemiological studies involving epigenomics, + transcriptomics, and genomics of diseases of pregnancy and + post-traumatic stress disorder. ++ Published results in scientific publications and presented results + orally at major scientific conferences. ++ Wrote and completed grants, including budgeting, scientific + direction, project management, and reporting. ++ Mentored graduate students and collaborated with internal and + external scientists. ++ Performed literature review, training, and applied new techniques to + maintain abreast of current scientific literature, principles of + scientific research, and modern statistical methodology. ++ Wrote software and designed relational databases using R, perl, C, + SQL, make, and very large computational systems ([Blue Waters](https://bluewaters.ncsa.illinois.edu/)) + +## Postdoctoral Researcher at USC 2013–2015 ++ Design, execution, and analysis of an epidemiological study to + identify genomic variants associated with systemic lupus + erythematosus using targeted deep sequencing. ++ Wrote multiple pieces of software to reproducibly analyze and + archive large datasets resulting from genomic sequencing. ++ Coordinated with clinicians, molecular biologists, and biologists to + produce analyses and major reports. + +## Postdoctoral Researcher at UCR 2010–2012 ++ Executed and analyzed an epidemiological study to identify genomic + variants associated with systemic lupus erythematosus using prior + information and array based approaches in a trio and cross sectional + study of individuals from the Los Angeles and greater United States. ++ Wrote and maintained multiple software components to reproducibly + perform the analyses. + # Education -## UC Riverside -+ **PhD** in Cell, Molecular and Developmental Biology -+ **BS** in Biology ++ Doctor of Philosophy (PhD) in Cell, Molecular and Developmental Biology at UC Riverside ++ Batchelor of Science (BS) in Biology at UC Riverside # Skills -## Genomics and Epigenomics -+ Genomics and Epigenomics of complex human diseases including - PTSD, Systemic Lupus Erythematosus, and Alzheimer's Disease using - cross-sectional and longitudinal experimental designs -+ Correcting for and experimental design to overcome multiple - testing, confounders, and batch effects using Bayesian and - frequentist methods approaches -+ Reproducible, scalable analysis using workflows on cloud- and - cluster-based systems on terabyte-scale datasets +## Leadership and Mentoring ++ Lead teams of PhD and MD scientists in multiple scientific and + industrial programs ++ Mentored graduate students and Outreachy and Google Summer of Code + interns ++ Former chair of Debian's Technical Committee ++ Head developer behind https://bugs.debian.org + +## Bioinformatics, Genomics, and Epigenomics ++ NGS and array-based Genomics and Epigenomics of complex human + diseases using RNA-seq, targeted DNA sequencing, RRBS, Illumina + bead arrays, and Affymetrix microarrays from sample collection to + publication ++ Reproducible, scalable bioinformatics analysis using make, + nextflow, and cwl based workflows on cloud- and cluster-based + systems on terabyte-scale datasets ++ Alignment, annotation, and variant calling using existing and custom + software, including GATK, bwa, STAR, and kallisto + Using evolutionary genomics to identify causal human variants ## Statistics -+ Statistical modeling -+ Addressing confounders and batch effects ++ Statistical modeling (regression, inference, prediction, and machine + learning in very large (> 1TB) datasets) using R and python. ++ Correcting & experimental design to overcome multiple testing, + confounders, and batch effects (both Bayesian and frequentist) + Reproducible research +## Software Development ++ Languages: python, R, perl, C, C++, python, groovy, sh (bash, POSIX, + and zsh), make ++ Collaborative Development: git, Jira, gitlab CI/CD, github actions, + Aha!, continuous integration & deployment, automated testing ++ Web, Mobile: Shiny, jQuery, JavaScript ++ Databases: Postgresql (PL/SQL), SQLite, Mysql, NoSQL + ## Big Data -+ Parallel and Cloud Computing -+ Inter-process communication: MPI, OpenMP, Hadoop ++ Parallel and Cloud Computing (slurm, torque, AWS, OpenStack, Azure) ++ Inter-process communication: MPI, OpenMP + Filestorage: Gluster, CEFS, GPFS, Lustre -+ Cloud based-infrastructure: Azure, AWS, Docker, cloud-init -+ Debian GNU/Linux system administration - -## Mentoring and Leadership -+ Mentored graduate students and Outreachy and Google Summer of Code - interns -+ Chairperson of the Debian Technical Committee -+ Head developer behind https://bugs.debian.org - -## Software Development -+ Languages: perl, R, C, C++, python, groovy, assembly, sh, make -+ Collaborative Development: git, travis, continuous integration, - automated testing -+ Databases: Postgresql (PL/SQL), SQLite, Mysql ++ Linux system administration + +## Applications and Daemons ++ Web: apache, ngix, varnish (load balancing/caching), REST, SOAP, + Tomcat ++ Build Tools: GNU make, cmake ++ Virtualization: libvirt, KVM, qemu, VMware, docker ++ VCS: git, mercurial, subversion ++ Mail: postfix, exim, sendmail, spamassassin ++ Configuration Infrastructure: puppet, hiera, etckeeper, git ++ Documentation: \LaTeX, confluence, emacs, MarkDown, MediaWiki, ikiwiki, trac ++ Monitoring: munin, nagios, icinga, prometheus ++ Issue Tracking: Debbugs, Request Tracker, Trac, JIRA ++ Office Software: Gnumeric, Libreoffice, \LaTeX, Word, Excel, + Powerpoint + +## Networking ++ Hardware, Linux routing and firewall experience, ferm, DHCP, + openvpn, bonding, NAT, DNHS, SNMP, IPv4, and IPv6. + +## Operating systems ++ GNU/Linux (Debian, Ubuntu, Red Hat) ++ Windows ++ MacOS ## Communication + Strong written communication skills as evidenced by publication record -+ Strong verbal and presentation skills as evidenced by presentation - and teaching record - -# Experience -## Research Scientist at UIUC -+ 2015–Present. University of Illinois at Urbana-Champaign. Epigenetic - modifications associated with PTSD, the genomic basis of the - development of parturition in mammals, and detecting adverse - pregnancy outcomes using urinary exosomes. - -## Postdoctoral Researcher at USC -+ 2013–2015. Identifying genes and causal alleles associated with - Systemic Lupus Erythematosus using genome-wide association, - next-generation sequencing, computational and biochemical - approaches. - -## Postdoctoral Researcher at UCR -+ 2010–2012. Identifying genes which are associated with Systemic - Lupus Erythematosus using prior information and targeted trio-based - studies. - -## Debian Developer -+ 2004–Present. *Debian Project*, Developer; Technical Committee - Member (2010–2016), Technical Committee Chair (2015–2016). - -# Authored Software -+ **[Debbugs](http://bugs.debian.org)**: Bug tracking software for the Debian GNU/Linux - distribution. -+ **[CairoHacks](https://git.donarmstrong.com/r/CairoHacks.git)**: - Bookmarks and Raster images for large PDF plots in R. -+ **[Function2Gene](http://rzlab.ucr.edu/function2gene/)**: Gene - selection tool based on literature mining which enables Bayesian - approaches to significance testing. -+ **[Helical Wheel Projections](http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit)**: - Web-based tool to draw helical wheel protein projections. - - -# Publications and Presentations -+ 20 peer-reviewed refereed publications cited over 1700 times: - -+ Publication record in GWAS, expression analysis of microarrays, - epigenetics, comparative evolution of mammals, and lipid membranes -+ H index of 11 ++ Strong verbal and presentation skills as evidenced by presentation, + leadership, and teaching record + +# Authored Open Source Software ++ *[Debbugs](http://bugs.debian.org)*: Bug tracking software for the Debian GNU/Linux + distribution. ++ *[CairoHacks](http://git.donarmstrong.com/r/CairoHacks.git)*: Bookmarks and Raster images for large PDF plots in R. +* Publications and Presentations ++ 24 peer-reviewed publications cited over 3000 times: + https://dla2.us/pubs ++ Publication record in GWAS, transcriptomics, SLE, GBM, epigenetics, + comparative evolution of mammals, and lipid membranes ++ H index >= 20 + Multiple presentations on EWAS of PTSD, genetics of SLE, and Open - Source: + Source: https://dla2.us/pres # Funding and Awards ## Grants -+ 2017 R Consortium: - **[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)** - Role: Co-PI -+ 2015 Blue Waters Allocation Grant: **Making ancestral trees using Bayesian - inference to identify disease-causing genetic variants** Role: ++ 2017 R Consortium: *[Adding Linux Binary Builders to R-Hub](https://www.r-consortium.org/blog/2017/04/03/q1-2017-isc-grants)* Role: + Co-PI ++ 2015 Blue Waters Allocation Grant: *Making ancestral trees using Bayesian + inference to identify disease-causing genetic variants* Role: Primary Investigator -+ **Tracking placenta and uterine funciton using urinary extracellular vesicles** (R21 ++ *Tracking placenta and uterine funciton using urinary extracellular vesicles* (R21 RFA-HD-16-037) Role: Key Personnel -+ **NIAMS** R01-AR045650-04 **Genetics of Childhood Onset SLE** to Chaim O. Jacob. ++ *NIAMS* R01-AR045650-04 *Genetics of Childhood Onset SLE* to Chaim O. Jacob. Role: Key Personnel ## Scholarships and Fellowships -+ 2001--2003: University of California, Riverside Doctoral Fellowship -+ 1997--2001: Regents of the University of California Scholarship. ++ 2001–2003: University of California, Riverside Doctoral Fellowship ++ 1997–2001: Regents of the University of California Scholarship. -#Academic Information +# Academic Information You can also read my [Curriculum Vitæ](curriculum_vitae) ([pdf](dla-cv.pdf)), [Research Statement](research_statement)